Delete the Matrix
by musingofmychoosing
Summary: Description: This story is my version of what happened after Neo discovered his powers and defeated Agent Smith in the first Matrix movie and kisses Trinity. It's takes place about maybe 24 hours later after Neo and the rest of the crew has rested and stu
1. Default Chapter

Disclaimer: I did not create these characters and they are based off the Matrix movies etc.

Me: I have not read any Matrix fanfics. This is also my first fanfic. I will take some ideas from the movies, but I will change and add my own. This is my version after all. If you read this, please review and comment on it. Please excuse any typos, my PC is acting up and I can't use spellcheck.

Description: This story is my version of what happened after Neo discovered his powers and defeated Agent Smith in the first Matrix movie and kisses Trinity. It's takes place about maybe 24 hours later after Neo and the rest of the crew has rested and stuff.

**Delete the Matrix**

Chapter 1: Re-Enter the Matrix

Neo quietly and slowly left his bedside so as not to wake-up Trinity. He sat down on a stool beside her. It had been awhile since he had a good night's sleep. But it had been difficult to sleep after what had occured the past day. He had finally learned to see past the Matrix and manipulate it as he wished. He had done the unthinkable and defeated a sentinel. Everything had happened so fast. He had been freed from the mental prison that is the Matrix and entered the real world. It wasn't exactly a pretty world, but it was the true physical world. He had aslo found true love with Trinity and a true concern for the people still trapped in the Matrix. As he left the room he hoped that the others would be awake now.

Morpheus and Tank were already awake looking at computer screens into the Matrix. "Do you guys ever sleep?" he asked. Morpheus jumped a little "Neo!...you startled me... I hope you are rested". "Yes, as much as I can be right now", Neo saw that there was a concerned look in Morphues' face, "What's the matter?"

Tank quickly explained the situation, "The Matrix is changing, the machines are up to something. Now that they know you exist they must be thinking of a plan to counter-attack. But we have no clue what they are planning....we expected something like this, but ...it's just that the codes are changing really fast...I can't read the changes"

"What do we do now?" Neo asked Morpheus.

"We must stop the Matrix now and the only way is for people to see the truth Neo. Neo you must show them the truth and we can't lose any more time." All three men were full with anxiety, the screen only showed bits and parts of the Matrix at a time. Neo couldn't quite figure out what was happening either. But, Neo felt ready to do whatever was necessary, he feared nothing in the Matrix.

"All right, hook-me up, I'll go in alone. Let's hurry".

In less than a minute Neo was hooked into the Matrix. He was ready for the battle of his life. The moment had arrived to destroy the Matrix. He wasn't sure how, but he wanted the machines to know it was time to fight and Neo wanted them to know it

" I know you're out there. I can feel you now. I know that you're afraid... you're afraid of us. You're afraid of change. I don't know the future. I didn't come here to tell you how this is going to end. I came here to tell you how it's going to begin. I'm going to hang up this phone, and then I'm going to show these people what you don't want them to see. I'm going to show them a world without you. A world without rules and controls, without borders or boundaries. A world where anything is possible. Where we go from there is a choice I leave to you."

He stepped out of the phone booth, put his sunglasses on and took a look at the people he hoped would be free soon. Then in a split second he flew fast into the air. He could see the codes in the Matrix. His mind was free from it's laws. He could travel and manipulate the Matrix as he pleased. But suddenly he heard Trinity's voice.

"Neo stop! get back here hurry!". Neo quickly flew back to the booth and left the Matrix.

"What's the matter Trinity, what happened?" Neo was worried, but he couldn't see what was wrong.

"I'm sorry Neo, I don't agree with the way you all are handling this"

"Trinity we have no choice, we don't know what the machines are planning. We have to act now!" yelled Morpheus, he was furious with Trinity.

"I understand, but think about the people"

"We ARE thinking about the people!" fumed Morpheus.

"Look what happened with Cypher!," trinity shouted as she pointed to the area where their friends lay dead. Dozer, Apoc, Switch, Mouse, and Cypher himself had been killed because of his betrayal. Trinity continued, " How do you think people will react to the truth? Even Neo couldn't accept the truth at first!," they stood in silence for a few seconds. Cypher had almost killed them all. He hated the real world and he wished he had never knew about it. he was willing tolive in the fake figmentations produced by the Matrix then live in the real world. Trinity hated Cypher for betraying them, but at the same time she could understand how he felt. She was happy that someone like Neo had been found, but that horrible event caused her to re-think her viewpoints. Neo finally broke the silence.

"Morpheus....I think Trinity is right. Let us try to calm down and think this through" Morpheus sat down and covered his face with his hands.

"I'm worried...I'm sorry Trinity...but the Matrix is drastically changing....you know they are up to something...."

"Yes, but we're already heading back to Zion. We can discuss this with the Council members? We haven't even told the members about what happened here and about Neo"

"And wait that long?....we have to do something NOW!"

"Then we'll think of that something, but please I don't think we should wake those that are not ready". Again there was silence. Trinity had a strong stance, but Neo could also see the concern in her eyes. She was strong, she was a fighter, but also caring. Morpheus sighed and slowly nodded.

"Very well Trinity...hopefully we'll soon get an idea of what the machines are up to. But we still have to act soon. We'll try to contact other ships and get word to Zion about our situation."

- ---- ---------- ------- --- - - - - ------------ ----------------

Contact with the ship Mercury had been made. The crew of the Mercury couldn't believe that the prophecy had been fullfilled and that someone existed who could potentially destroy the Matrix and the machines. It was a surreal and sad moment for everyone. After so many years, never sure if that person would ever exist and now here he was. They were full of hope, but also uncertain about the next step to take. The news of neo and the deaths of their companions were sent to other ships. The Nebuchadnezzar crew had settled down after awhile and was eating. Neo hoped that they would figure something out. Morpheus was the first to approach the subject.

"I always thought that once I found Neo, we would end the Matrix and the machines right away. I don't know how many are ready to wake up, but we must start freeing those that are ready. I hope now that we have Neo, it will be easier and faster."

"Are there any in this region that we can free soon?" Neo asked.

"Yes...we have many persons that seem ready to leave the Matrix. It's just that the risk and danger in these missions made it slow work" Trinity remarked, she was quiet a moment and then continued "...many like you feel that they are in a dream world. Somewhere in their mind they feel it...they know it's fake and they want to escape. But, we try to free those that are still young because as you know....it's easier for them to accept the truth.....and usually we pick those that have no family or very strong attachments to others...otherwise it's hard to let go," Trinity's tone was so sad. Neo had no family or real friends in the Matrix. But he didn't know if it was true for Trinity. She was such a caring person, he couldn't imagine her being a loner like he was. Could it be that she had left family or someone special behind? Neo answered quickly, "Then maybe we should start on that"

"I think in a couple of days we can get everything ready and free someone soon,"exclaimed Morpheus.

"No Morpheus, I'll do it alone. I don't want you guys in danger. I think I can handle it."

"No Neo we should go as group, just in case" said Trinity who didn't think it was safe to go alone yet. Neo thought for a moment and then came up with an idea.

"How about if I go in the Matrix for a few minutes....in a place that has many exits so that I can escape easily. Maybe I'll be able to see what is changing in the Matrix and also if the sentinels will detect me and if they will attack. It'll be a test"

"Neo don't take this lightly" pleaded Trinity.

"Please Trinity, let me do this first.... I don't want you guys there if it's more dangerous now" Trinity was reluctant, but knew he was right and agreed.

-- - - - ------------ - - - --------------- - - - - ------------ - ----

After some time, Tank finally found a location that had exits that Neo could reach easily. Neo studied the area as best as he could. It helped Trinity be less nervous. Morpheous on the other hand was very confident of Neo. The following day Neo was ready and was hooked-up. Again he entered the Matrix.

Once he was in the Matrix, Neo headed for the nearest exit. This was only to test out the area so he only wanted to stay a few minutes. Trinity, Morpheous, and Tank read the computer screens and followed Neo's actions as best as they could. Neo walked on the streets and at first things seemed normal. But there was hardly a single person on the streets. It was late in the afternoon and rarely anyone in sight. He became alarmed and decided to quickly go to the nearest exit which was located in a nearby bar. The bar was closed, but Neo knocked hoping someone would open.

The owner peered through the door, "Sorry we won't be opening"

"It's okay, I just want to use your phone please"

The bar owner seemed a bit nervous and paused a bit, "Okay, but hurry"

As Neo entered the bar he hoped he could get some answers about the lack of people "Sir, why won't you be opening the bar today?"

The bar owner pointed to the news on the t.v. "It's getting worse". Neo stopped to listen to the news report that was airing.

"...scientist say that what they know about this mysterious disease is that it attacks the nervous system first. In almost all the cases victims have been reported to have violent sudden convulsions then they go into a coma and eventually leading to their deaths. The number of deaths worldwide is in the hundres of thousands and it is believed that thousands more have been infected. Although the mode of infection has not been discovered..."

"What? How could this have happened so quickly? Where is this happening?" Neo asked the owner. He was shocked and worried.

"The new cases? They are happening in states nearby. I thought maybe this was just gonna be in Asia and all those other countries. But I guess with people traveling in planes and all that...it just spreads faster. Hope that now that we know some of the symptoms they can quarantine and contain it over there."

"You're kidding me, that's impossible, how can it travel so fast. It's been only a couple of days!"

"Well yeah, but they probably had the virus for awhile before the symptoms showed up"

Neo couldn't understand this. Was this what the machines were up to? But why would they start killing off people, they needed the people for their energy. But he could feel that the machines were behind this. He was filled with horror, disbelief, and dread. Neo ran to the back of the bar where the phone booth was located he called Tank on his cell phone, "Tank I gotta get outta here, hurry!".........

- - - Okay that's the first chapter. Are the machines behind all this? I wish I had written the second chapter, but it takes so long so I have to post it non. Hope to write more, please leave feedback and reviews.


	2. Chapter 2

"What the hell happened?," Tank asked Neo while unhooking him from the Matrix program. Neo's eyes were wide and he was breathing heavily. Tank continued "I didn't read any sentinels on the scene,what happened in there?." Trinity and Morpheous were also concerned.

"Neo calm down," Trinity held Neo's hand and Neo slowly began to calm down.

"I just don't get it...this is something the machines are up too...I know it...I feel it...but it doesn't make sense...why?," It was a concept that was hard for Neo to grasp and his mind was racing and searching for an answer. Finally he started telling the crew what he just learned, "There's a worldwide virus, an emerging epidemic, it's causing people to die. I know it's happened before in history, but this has happened in the past couple of days...and I know it's the machines. They are doing this on purpose, but I don't understand why."

Trinity was completely shocked, they all looked at Morpheus as though he could supply some answer. He had always guided them, but he was just as baffled as they were. He thought for a moment and then asked, "What is this virus like?"

"Not much is known yet. Usually the victims experience convulsions, then they go into a coma and then they eventually die, I think this all happens pretty quickly," Morpheus was thinking about this information Neo provided. He was confused, but there were some ideas floating in his head. He didn't want to voice them until he had more information.

"Tank let's contact the Mercury and see if anyone has any new information," Tank quickly followed his orders. Captain ...

"Morpheus, I hope you are all doing well today. Have you heard about what is happening in the Matrix?"

"About the virus"

"Yes"

"Neo just came back from the Matrix with the news. He believes that the machines are responsible, but we can't figure out why. Has anyone been to the Sleep Suspension locations or any other areas?"

"Yes, we sent ...ships to check out the some of the Sleep Suspension areas. I hope that they return safely. I'll communicate anything new as soon as we have some news."

"Thank you ... may everything go well," Morpheus ended the communication. He thought for a moment and sighed, "I suppose we can only wait now, but let us see if we can do anything else."

"What are the Sleep Suspension areas?" Neo asked. Since he was freed from the Matrix, many months were spent on his recuperation. It had only been a few days that he was truly "awake" and receptive to his new environment and in that short period he had fullfilled the prophecy. But he didn't know much about Zion and the Rebellion."

Trinity explained,"The Sleep Suspension areas is where the people are hooked up into the Matrix, where we were kept before being freed. Do you remember them Neo?" Neo recalled the moment he was unplugged from the Matrix by a machine. Moments before that he had seen endless columns with people in some sort of capsule. All of them hooked into the Matrix. It was a horrific memory, "Yes, unfortuanetly I do remember."

"It's very dangerous to go there Neo. Machines are there plugging new people in and removing the dead or awaken and securing the area. But we have to see what they are doing right now. The area is massive, I hope the ships will be able to see what is happening," Morpheus said. They stood silent for a moment. Neo wanted to stop the machines. 'But what can I do?' he asked himself, he needed to do something now. He needed to stop the virus. But it would be difficult doing that because the Matrix was extensive. The virus was just a code. He kept thinking about that and then an idea came to him. Maybe he couldn't stop it completely, but he might be able to help.

"The virus is only a code, I can see the Matrix and it's codes. I think I can neutralize it in the people who already have the virus. I have to go in now" Neo was excited about his idea. Everyone else was surprised, but they thought it could also work. "I need to go to Asia first, I think that's where it started and it's the area most affected I think."

"Man, that's a good idea Neo," Tank exclaimed. Trinity gave a faint smile as she turned towards Morpheus waiting for his approval. Morpheus smile and nodded. Tank quickly walked to the computers,"Alright then. Neo let's get going...let me see...okay here they are...you'll be speaking Cantonese, Japanese, and whole lot more in no time." Trinity helped Neo hook-up. Everything was done quickly.

"Good luck Neo, I believe in you," Trinity told Neo.

"Arigato," he said with a smile. Then he was into the Matrix.

Neo had picked an area near a hospital. He hadn't planned much out and he hoped that it would all work. He entered the hospital and asked a nurse if there were people with that new virus. There were indeed many infected individuals. Ofcourse they weren't going to let him just walk in. He tried saying he was a forieng doctor who might help. The nurse looked at him funny and stared at his black trenchcoat. Neo mentally scolded himself for wearing it on this mission. A doctor passed by a Neo tried to convince him as well. They disn't want to, but Neo said he had a cure. They reluctantly let him see a patient. The doctor and another nurse were in the room with Neo. The patient was already in a coma. Neo observed him. He was searching for the virus code, he needed to see what it was like in order to recognize it and help others that might have it. He found it. All he had to do was manipulate it, destroy it. It was all part of the Matrix. He placed his hand on the patient's forhead. The doctor and nurse didn't expect that, but in a couple of seconds the virus was gone. Then a moment later, the patient opened his eyes and sat up. The doctor and nurse were stunned. The patient didn't even know what was going on or how he ended up in a hospital. Neo smiled and still looking at the patient he said, "Bring me the others with this disease...hurry please." The doctor still stood there speechless and the nurse quickly ran out, she thought he was some sort of witch doctor. Whoever he was, she only hoped that he would help them.

Trinity, Tank, and Morpheus were trying to see what was going on. Something for sure was changing. Then they heard Neo tell them, "You guys, it's working."


End file.
